Structure of arabidopsis dirigent protein ATDIR6

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 57% strand (DSSP).

Ligands and binding sites

• GLY · Glycine · ligand · 5 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
• MAN · alpha-D-mannopyranose · sugar · 6 copies · chains B
• BMA · beta-D-mannopyranose · sugar · 3 copies
• XYP · beta-D-xylopyranose · sugar · 3 copies · chains A, B
• FUC · alpha-L-fucopyranose · sugar · 3 copies · chains B, A
• EDO · 1,2-ethanediol · additive · 8 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 460 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

• 5LAL · Structure of Arabidopsis dirigent protein AtDIR6 · the same entry in another collection · chain A against A, TM-score 1.00
• Q9SUQ8 · AlphaFold monomer V2.0 prediction for dirigent protein 6 (Q9SUQ8) · a predicted model of the same protein · chain B against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q9SUQ8
• Elsewhere: RCSB PDB 5LAL · PDBe 5LAL · UniProt Q9SUQ8